[ome-devel] Help with writing OME-TIFF

[Curtis Rueden]

Hi Stuart,

> I'm attempting to add support for OME-TIFF export to my software
> (ilastik).

Wonderful! :-)

> - The original file has dimensions XYCZT, but 'C' and 'T' have size 1.
> In my version, I just omit those axes.  Is that permitted under the
> standard?

Nope. According to the OME-XML schema, the DimensionOrder attribute is an
enumeration which must have a valid five-digit value; see:

https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_DimensionOrder

Instead of writing "XYZ" try writing "XYZCT" (or "XYZTC"; doesn't really
matter since you only have 1 C and 1 T position).

> - The original file has 'ROI' entries in the metadata.  I'm omitting
> that information.  Is that standards-compliant?

It is not required to include ROI information. See the "minimum
specification" for a compliant file:

http://www.openmicroscopy.org/site/support/ome-model/specifications/minimum.html

Note that your XML is much more complex than necessary, because you are
writing a single-file OME-TIFF. As long as your IFDs are in Z-ascending
order, you can simply write:

<?xml version="1.0" encoding="UTF-8"?>
<!-- Warning: this comment is an OME-XML metadata block, which
contains crucial dimensional parameters and other important metadata.
Please edit cautiously (if at all), and back up the original data
before doing so. For more information, see the OME-TIFF web site:
http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. -->
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2015-01"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2015-01
http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd">
  <Image ID="Image:0" Name="exported-data">
    <Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0"
SizeX="400" SizeY="300" SizeZ="4" Type="uint8">
      <Channel ID="Channel0:0" SamplesPerPixel="1">
        <LightPath />
      </Channel>
      <TiffData />
    </Pixels>
  </Image>
</OME>

And the mapping from IFDs to ZCT coordinates will be inferred as desired.

Lastly, you saw the OME-TIFF specification page, right?
http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/specification.html

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Jul 28, 2016 at 4:02 PM, Berg, Stuart <bergs at janelia.hhmi.org>
wrote:

> Greetings,
>
> I'm attempting to add support for OME-TIFF export to my software
> (ilastik).  Since writing the OME-TIFF header seems simple enough (for
> simple cases, anyway), I want to avoid using an external library like
> python-bioformats.
>
> But apparently I'm doing something wrong, because the files I'm producing
> can't be read correctly by the Fiji BioFormats plugin.  I'd appreciate it
> if someone can tell me what I'm doing wrong.  I've attached two files.  One
> is a valid OME-TIFF file, and the other is my "converted" version of it
> (same data, but the XML header was written by my software).  The OME header
> from my version is pasted below.
>
> When I use the BioFormats Importer to read my 'converted' file, the header
> seems to be ignored, and instead BioFormats guesses that the file is a
> T-stack, not a Z-stack as I intended.
>
> Questions:
> - The original file has dimensions XYCZT, but 'C' and 'T' have size 1.  In
> my version, I just omit those axes.  Is that permitted under the standard?
> - The original file has 'ROI' entries in the metadata.  I'm omitting that
> information.  Is that standards-compliant?
>
> Best regards,
> Stuart
>
> PS — The
>
> Here's the header I'm writing.  If you spot any obvious errors, let me
> know.
>
> <?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2015-01" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" UUID="urn:uuid:5cb6938c-5503-11e6-ade4-a45e60e933fb" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2015-01 http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd">
>   <Image ID="Image:0" Name="exported-data">
>     <Pixels BigEndian="true" DimensionOrder="XYZ" ID="Pixels:0" SizeX="400" SizeY="300" SizeZ="4" Type="uint8">
>       <Channel ID="Channel0:0" SamplesPerPixel="1">
>         <LightPath />
>       </Channel>
>       <TiffData FirstZ="0" IFD="0" PlaneCount="1">
>         <UUID FileName="xyz-converted.ome.tiff">urn:uuid:5cb6938c-5503-11e6-ade4-a45e60e933fb</UUID>
>       </TiffData>
>       <TiffData FirstZ="1" IFD="1" PlaneCount="1">
>         <UUID FileName="xyz-converted.ome.tiff">urn:uuid:5cb6938c-5503-11e6-ade4-a45e60e933fb</UUID>
>       </TiffData>
>       <TiffData FirstZ="2" IFD="2" PlaneCount="1">
>         <UUID FileName="xyz-converted.ome.tiff">urn:uuid:5cb6938c-5503-11e6-ade4-a45e60e933fb</UUID>
>       </TiffData>
>       <TiffData FirstZ="3" IFD="3" PlaneCount="1">
>         <UUID FileName="xyz-converted.ome.tiff">urn:uuid:5cb6938c-5503-11e6-ade4-a45e60e933fb</UUID>
>       </TiffData>
>     </Pixels>
>   </Image></OME>
>
>
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